import org.forester.archaeopteryx.TreePanel;
import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.PhylogenyData;
-import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.ProteinDomain;
import org.forester.util.ForesterUtil;
public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData {
+ final static private String SPECIAL_DOMAIN = "RRMa";
final static private int BRIGHTEN_COLOR_BY = 200;
final static private int E_VALUE_THRESHOLD_EXP_DEFAULT = 0;
final static private BasicStroke STROKE_1 = new BasicStroke( 1f );
private final DomainArchitecture _domain_structure;
private int _e_value_threshold_exp = E_VALUE_THRESHOLD_EXP_DEFAULT;
private final Rectangle2D _rectangle = new Rectangle2D.Float();
- private double _rendering_factor_width = 1.0;
- private double _rendering_height = 0;
+ private float _rendering_factor_width = 1;
+ private float _rendering_height = 0;
+ private String _node_name;
public RenderableDomainArchitecture( final DomainArchitecture domain_structure ) {
_domain_structure = domain_structure;
}
+ public RenderableDomainArchitecture( final DomainArchitecture domain_structure, final String node_name ) {
+ _domain_structure = domain_structure;
+ _node_name = node_name;
+ }
+
public static void setColorMap( final Map<String, Color> domain_colors ) {
_domain_colors = domain_colors;
}
}
for( double i = 0; i < heigth; i += step ) {
g.setColor( org.forester.util.ForesterUtil
- .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) );
+ .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) );
+ _rectangle.setFrame( x, i + y, width, step );
+ g.fill( _rectangle );
+ }
+ }
+
+ private final void drawDomainGrey( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final String name,
+ final Graphics2D g,
+ final boolean to_pdf ) {
+ final double h2 = heigth / 2.0;
+ final Color color_one = Color.GRAY;
+ final Color color_two = getColorTwo( color_one );
+ double step = 1;
+ if ( to_pdf ) {
+ step = 0.05;
+ }
+ for( double i = 0; i < heigth; i += step ) {
+ g.setColor( org.forester.util.ForesterUtil
+ .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) );
_rectangle.setFrame( x, i + y, width, step );
g.fill( _rectangle );
}
return new Integer( _e_value_threshold_exp );
}
- public double getRenderingFactorWidth() {
+ public float getRenderingFactorWidth() {
return _rendering_factor_width;
}
}
@Override
- public void render( final double x1,
- final double y1,
+ public void render( final float x1,
+ final float y1,
final Graphics2D g,
final TreePanel tree_panel,
final boolean to_pdf ) {
- final double f = getRenderingFactorWidth();
- final double y = y1 + ( _rendering_height / 2 );
- final double start = x1 + 20.0;
+ final float f = getRenderingFactorWidth();
+ final float y = y1 + ( _rendering_height / 2 );
+ final float start = x1 + 20;
final Stroke s = g.getStroke();
g.setStroke( STROKE_1 );
if ( !to_pdf ) {
}
_rectangle.setFrame( start, y - 0.5, _domain_structure.getTotalLength() * f, 1 );
g.fill( _rectangle );
+ short special_domain_count = 0;
for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) {
final ProteinDomain d = _domain_structure.getDomain( i );
- if ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) {
- final double xa = start + ( d.getFrom() * f );
- final double xb = xa + ( d.getLength() * f );
+ if ( ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) )
+ || ( TreePanel.SPECIAL_DOMAIN_COLORING && ( d.getName().equals( SPECIAL_DOMAIN ) ) && ( ( d
+ .getConfidence() <= 1 ) ) ) ) {
+ if ( TreePanel.SPECIAL_DOMAIN_COLORING && ( d.getName().equals( SPECIAL_DOMAIN ) ) ) {
+ special_domain_count++;
+ }
+ final float xa = start + ( d.getFrom() * f );
+ final float xb = xa + ( d.getLength() * f );
if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels()
&& ( tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getHeight() > 4 ) ) {
g.setFont( tree_panel.getMainPanel().getTreeFontSet().getSmallFont() );
else {
g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF );
}
- PhylogenyDataUtil.drawString( d.getName(), xa, y1
- + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
- + _rendering_height, g );
+ g.drawString( d.getName(), xa, y1
+ + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
+ + _rendering_height );
+ }
+ if ( TreePanel.SPECIAL_DOMAIN_COLORING && ( _node_name.indexOf( "~" ) > 1 )
+ && ( d.getName().equals( SPECIAL_DOMAIN ) )
+ && ( _node_name.indexOf( "~" + special_domain_count + "-" ) < 1 ) ) {
+ drawDomainGrey( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
+ }
+ else {
+ drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
}
- drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
}
}
g.setStroke( s );
_e_value_threshold_exp = ( int ) e_value_threshold_exp;
}
- public void setRenderingFactorWidth( final double rendering_factor_width ) {
+ public void setRenderingFactorWidth( final float rendering_factor_width ) {
_rendering_factor_width = rendering_factor_width;
}
@Override
- public void setRenderingHeight( final double rendering_height ) {
+ public void setRenderingHeight( final float rendering_height ) {
_rendering_height = rendering_height;
}